Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa

Authors: ZHANG, FAN - Chinese Academy Of Agricultural Sciences; LONG, RUCAI - Chinese Academy Of Agricultural Sciences; MA, ZHIYAO - Chinese Academy Of Agricultural Sciences; XIAO, HUA - Chinese Academy Of Agricultural Sciences; XU, XIAODONG - Chinese Academy Of Agricultural Sciences; LIU, ZHONGJIE - Chinese Academy Of Agricultural Sciences; WEI, CHUNXUE - Chinese Academy Of Agricultural Sciences; WANG, YIWEN - Chinese Academy Of Agricultural Sciences; PENG, YANGLING - Chinese Academy Of Tropical Agricultural Sciences; YANG, XUANWEN - Chinese Academy Of Agricultural Sciences; SHI, XIAOYA - Chinese Academy Of Agricultural Sciences; CAO, SHUO - Chinese Academy Of Agricultural Sciences; LI, MINGNA - Chinese Academy Of Agricultural Sciences; XU, MING - Chinese Academy Of Agricultural Sciences; HE, FEI - Chinese Academy Of Agricultural Sciences; JIANG, XUEQIAN - Chinese Academy Of Agricultural Sciences; ZHANG, TIEJUN - Beijing Forestry University; WANG, ZHEN - University Of Nebraska; Li, Xianran; Yu, Long-Xi; YANG, QINGCHUAN - Chinese Academy Of Agricultural Sciences

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2024
Publication Date: 6/3/2024
Citation: Zhang, F., Long, R., Ma, Z., Xiao, H., Xu, X., Liu, Z., Wei, C., Wang, Y., Peng, Y., Yang, X., Shi, X., Cao, S., Li, M., Xu, M., He, F., Jiang, X., Zhang, T., Wang, Z., Li, X., Yu, L., Yang, Q. 2024. Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa. Molecular Plant. 17(6):867-883. https://doi.org/10.1016/j.molp.2024.04.013.
DOI: https://doi.org/10.1016/j.molp.2024.04.013

Interpretive Summary: In this study, we constructed a genomic variance map of 702 accessions consisting of 24 Medicago species. The population genetic analysis revealed that a mixed population of two Medicago species differentiated from the self-pollinated single species but there was genetically similarity within the mixed population. The divergence between two species, M. sativa and M. falcata ,was lowest compared to other Medicago species. Genes causing this divergence included those causing stress response, such as temperature and light response genes. Introgression of M. falcata increased the genetic diversity of alfalfa and helped alfalfa spread to Europe, North America, and East Asia, but deleterious genes were introgressed as well. The genes selected for adaptation during the spread of alfalfa from M. falcata were identified in the study. This allows us to predict where alfalfa should do well in the future considering climate change modeling scenarios. We show that fast migration will be needed to offset global environmental change to allow optimal alfalfa production worldwide. The geographic center of origin of alfalfa is predicted to serve as a refuge for the survival of alfalfa in varied environmental conditions in our studies and should be protected.

Technical Abstract: Climate change is a major threat to global food security. A large-scale and detailed population vulnerability estimation is crucial for the impacts of climate change on crop productivity and sustainability. Here, we analyze genomic resequencing data of 702 accessions consisted of 24 species of Medicago, a genus including model plant Medicago truncatula and alfalfa (Medicago sativa L.). We found cross-pollination Medicago sativa-falcata species complex is highly diverged with other self-pollination Medicago species. Introgression of Medicago falcata contributed to the worldwide adaption of alfalfa but introduced more genetic burden. A total of 1671 environmental-adapted genes were identified during adaption, including stress response and reproductive related genes. Introgression contributed to 9.9% of environmental-adapted genomic regions. Global environmental change speed and migration could seriously affect the distribution areas of alfalfa, especially high latitude of the northern hemisphere. Gene flow among Medicago species certify certifies that attenuate the impact of climate change could from interspecific, inter-subspecific and intraspecific level. Our study on the history of alfalfa evolution, present genomic responses to environmental factors, and future adaptive prediction provide new insight toward breeding comprehensive strategies for breeding alfalfa varieties enhanced climate resilient.